AndreaBozzo/ceres-open-data-index huggingface dataset:
Experimental data set of cover crop mixture and weed control in tropical summer and winter in Reunion Island.

[Lien vers la fiche source] Weed pressure is a main biotic constraint in tropical agriculture. Cover crop mixtures have increased in popularity to limit weed growth through competition for shared resources but the relation between cover crop diversity and weed suppression is still under debate. This study aimed to assess the impact of increasing cover crops diversity (one to four species) on weed control during two 4-month growing seasons (tropical summer and winter) in Reunion Island. Weed control was expressed in terms of ground cover by weeds and weed aboveground dry mass and linked to cover crop traits in the mixtures.
Qualitative data for analysis: semi-directive interviews about Covid-19 pandemic perception and management in Reunion Island in 2021

[Lien vers la fiche source] These data represent the different perception of Covid-19 and its management in Reunion Island. The corpus constitutes qualitative data obtained via semi-directive interviews of 53 participants which took place early 2021. The study questions the brakes and motors of adherence to health measures in order to inform public authorities in their current and future approaches to COVID or other future health crises.
Spectroscopic (VIS-NIR) analysis of organic resources with animal, agro-industrial, and urban origins collected from different regions of Madagascar

[Lien vers la fiche source] VIS-NIR spectra of organic resources collected in Madagascar from livestock, urban or agrobusiness origins. Detailed description of origin, animal species, by-products types, and compositional analysis are at https://doi.org/10.18167/DVN1/YRMQ52
Compositional analysis of organic resources with animal, agro-industrial, and urban origins collected from different regions of Madagascar

[Lien vers la fiche source] This dataset is a compilation of chemical analysis of organic wastes, so called organic resources (OR) collected during different studies in Madagascar (2009-2012). These materials include animal manures (piglet, pig, barrow, sow, broiler, chick, hen, cow, heifer, zebu bull, rabbit, pigeon, and sheep); urban wastes (raw municipal waste, composted municipal waste, vermicompost); agro-industrial by-products (bone, horn, blood, shell, cotton cake, peanut cake, groundnut cake, and tobacco ash) and mixed wastes (mixtures of animal, urban and/or agro-industrial origins). Chemical properties were analysed following laboratory standards.
Pluviométrie en zone cotonnière sénégalaise de 2000 à 2018

[Lien vers la fiche source] Données de pluviométrie mesurées à partir de 15 pluviomètres à lecture directe des services de l'agriculture du Sénégal et de la Société de Développement et des Fibres Textiles (SODEFITEX). Pluviomètres répartis sur l'ensemble de la zone cotonnière. Données relevées de 2000 à 2018.
Ontologie du risque

[Lien vers la fiche source] Ce jeu de données présente les travaux de modélisation du risque conduits dans l'Unité Espace-Dev. L'objectif est de proposer un premier jeu de modèles ontologiques autour du risque et de les faire évoluer par l'ensemble des membres de l'Unité. Les fichiers diffusés sont au [format texte/n3]
Cartographie narrative pour la restitution de travaux de modélisation des risques de transmission de maladies infectieuses

[Lien vers la fiche source] Les interfaces entre les aires protégées et leurs périphéries en Afrique australe sont sujettes à des interactions entre la faune et le bétail qui varient en fréquence et en intensité. Dans ces zones, la juxtaposition entre les utilisations des terres de production et de conservation dans un contexte d'enthronisation croissante peut créer des problèmes liés à la coexistence entre l'homme et la faune et soulève des préoccupations pour la conservation de la biodiversité, le développement local et les moyens de subsistance. Les interfaces sauvage/domestique jouent un rôle prépondérant dans l'émergence d'agents pathogènes (Despommier et al., 2006) en raison d'interactions importantes entre l'homme, les espèces domestiquées et la faune sauvage dans l'espace et dans le temps (Haydon et al., 2002). Ces transmissions d'agents pathogènes sont naturellement bidirectionnelles entre le réservoir et les populations sensibles (sauvage -> domestique vs domestique -> sauvage) et peuvent donc être potentiellement spatialisées autour de « points chauds » d'interactions espèces sauvages/domestiques. La proximité spatiale entre les populations a été clairement identifiée comme l'un des facteurs de risque cruciaux dans la transmission entre espèces (Roche et al., 2012). L'objectif principal est de modéliser à partir des données d'observation de la Terre, l'utilisation du paysage par les populations animales sauvages et domestiques pour mieux caractériser les contacts et leurs déterminants dans les zones d'interface sauvage/domestique et estimer le risque de transmission d'agents pathogènes.
Microplastic concentrations in river and reservoir environments of Dong Nai, Ho Chi Minh City, Long An and Tay Ninh provinces, Southern Vietnam. COMPOSE (2019-2021) and CounterMEASUREII (2021-2022) projects

[Lien vers la fiche source] Microplastic (300-5000µm) concentrations were measured in the Tri An reservoir and Dong Nai River of Dong Nai province, Saigon River of Ho Chi Minh City, Dau Tien reservoir of Tay Ninh province and Vam Co River of Long An province, Southern Vietnam, under the COMPOSE project (2019-2021) and the CounterMEASUREII project (2021-2022). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated on GF-A filter. Then microplastic were observed on stereomicroscope and length, area, color were measured for fragments, line and circle. Concentrations are given in total microplastic per m3, fragment per m3 and fibers per m3. The sampling dates are October 2019, January 2020, May 2020, July 2020, October 2020, January 2021 and March 2021 under COMPOSE Project; October 2021 and January 2022 under the CounterMEASUREII project.
Whole-genome genotyping data of 323 Beninese individuals followed for malaria infections and malaria-related phenotypes

[Lien vers la fiche source] This dataset consists of whole-genome genotyping data for 323 Beninese individuals followed for malaria infections and malaria-related phenotypes in north Benin. Study participants belong to the Fulani, Gando, Bariba, and Otamari ethnic groups and live in sympatry in four rural villages (Goufanrou, Gorgoba, Tamande, Kouboro) located 3-15 km apart, in the Birni district of the Atacora department, a region of northwestern Benin. Genotyping was performed on Illumina HumanOmni5-4v1 chips, in accordance with the standard protocol of Illumina Infinium HD assay. Standard quality control steps and criteria (Anderson et al. 2010) in GWAS were applied to data, resulting in a final set of 2,281,899 high-quality SNPs genotyped in 323 individuals.
Annotation of epidemiological information in animal disease-related news articles: guidelines and manually labelled corpus

[Lien vers la fiche source] This dataset contains two files: (i) An annotated corpus ("epi_info_corpus‧xlsx") containing 486 manually annotated sentences extracted from 32 animal disease-related news articles. These news articles were obtained from the database of an event-based biosurveillance system dedicated to animal health surveillance, PADI-web (https://padi-web.cirad.fr/en/). The first sheet (‘article_metadata’) provides metadata about the news articles : (1) id_article, the unique id of a news article, (2) title, the title of the news article, (3) source, the name of the news article website, (3) publication_date, the publication date of the news article (mm-dd-yyyy) and (4) URL, the web URL of the news article. The second sheet (‘annot_sentences’) contains the annotated sentences: each row corresponds to a sentence from a news article. Each sentence has two distinct labels, Event type and Information type. The set of columns is : (1) id_article, the id of the news article to which the sentence belongs, (2) id_sentence, the unique id of the sentence, indicating its position in the news content (integer ranging from 1 to n, n being the total number of sentences in the news article), (3) sentence_text, the sentence textual content, (4) event_type, the Event type label and (5) information_type, the Information type label. Event type labels indicate the relation between the sentence and the epidemiological context, i‧e. current event (CE), risk event (RE), old event (OE), general (G) and irrelevant (IR). Information type labels indicate the type of epidemiological information, i‧e descriptive epidemiology (DE), distribution (DI), preventive and control measures (PCM), economic and political consequences (EPC), transmission pathway (TP), concern and risk factors (CRF), general epidemiology (GE) and irrelevant (IR). (ii) The annotation guidelines ("epi_info_guidelines‧doc") providing a detailed description of each category.
Source code of CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

[Lien vers la fiche source] CulebrONT is an open-source, scalable, modulable and traceable snakemake pipeline, able to launch multiple assembly tools in parallel and providing help for choosing the best possible assembly. Documentation: [https://culebront-pipeline.readthedocs.io/en/2.1.1/] Code development: [https://github.com/SouthGreenPlatform/culebrONT] The authors acknowledge the IRD i-Trop HPC (South Green Platform) from IRD Montpellier for providing resources that contributed to this work.
Stakeholders' mental models about the Makay region, Madagascar

[Lien vers la fiche source] This dataset includes the mental models (in a matrix format) of 32 informants regarding the Makay region in Madagascar who were interviewed in 2019. For each individual informants, two files are available: (i) the raw mental model as elicited during the interview (in French) and (ii) the standardized mental model after homogenization across informants and translation into English. A notice is provided with all the variables used in the model and their associated codes. More information on the protocol and mental models' standardization is available in the associated publication. - Only anonymous data is provided. - Data does not include any sensitive information. - Participants provided verbal consent, which was documented by audio recording. - For all CSV files included in the dataset, columns/fields are separated by semi-colon character (;)
Soil, saltation and gradient method measurements acquired during the WIND-O-V project in 2017 and 2018, Tunisia

[Lien vers la fiche source] Data distributed here are part of the data acquired during the 2 field campaigns that were carried out in springs 2017 and 2018 in south Tunisia during the WIND-O-V project (https://www6.inrae.fr/anr-windov/) funded by the ANR. The distributed data document the characteristics of the 1) surface of the eroding field, 2) aerodynamic conditions (wind speed, stability of the surface boundary layer), 3) saltation flux (intensity and size-distribution), and 4) vertical dust flux (intensity and size-distribution) determined by the gradient method. The objective was to explore in depth and understand the links between all these parameters. Data include: (1) minimally-dispersed soil size distribution: soil samples were dried at 105°C during 24h before to be slowly sieved on a column of 14 sieves (<50, 50-63, 63-80, 80-100, 100-125, 125-160, 160-200, 200-250, 250-300, 300-400, 400-500, 500-800, 800-1000, >1000 µm). The duration of sieving was 20 minutes and the intensity 40 on a Retsch AS200 vibratory sieve shaker. Each fraction was then weighted on an electronic balance (0.0001 g of precision). (2) saltation flux: they were measured using five sand traps, the design of which was adapted from the Big Spring Number Eight (BSNE) of Fryrear (1986). Each sand trap had an opening of 5 x 10 cm². They were mounted on a mast with their centers positioned at 5.5, 20.25, 36.45, 51.20, and 87.25 cm above ground level (agl). The mast was equipped with a large wind vane so that the opening of all sand traps always faced the wind. After accounting for the collection efficiency of the sand traps, the saltation flux was computed by vertical integration of the cumulative masses collected at the 5 heights using the exponential formula proposed by Williams (1964). (3) aerodynamic parameters (16-min. average): aerodynamic roughness length, and stability parameters were estimated from the wind and temperature profiles using the iterative procedure designed by Frangi and Richard (2000). Wind speed and air temperature vertical profiles were determined using respectively 7 cup anemometers (A100R Vector Instrument®) positioned at 0.22, 0.65, 1.33, 1.83, 3.01, 4.00, and 5.24 m agl, and 4 thermocouples (type T cupper/Constantan) positioned at 0.48, 1.66, 3.83, and 5.07 m agl on the same mast. (4) vertical dust flux intensity and size distribution (16-min. average) were determined by the gradient method. Dust concentrations were measured using two identical Optical Particle Counters (OPC) welas® (White Light Spectrometer 2300, PALAS), each equipped with an omnidirectional total suspended particles (TSP) sampling head (BGI by Mesa Labs, Butler, NJ USA) installed at 2.04 m and 4.10 m agl.
Plastic bag regulation database for cross-country analyses

[Lien vers la fiche source] This dataset brings together the legal texts adopted by 10 entities regulating plastic bags: Cape Verde, England (UK), Florida (USA), France, Ireland, Scotland (UK), State of Pernambouco (Brazil), State of São Paulo (Brazil), and Texas (USA). The database facilitates the comparison of these texts, which can be accessed through their regulated objects, the design of the political instrument, the provided controls or sanctions.
Microplastic concentrations in riverine environments of Hanoi, Northern Vietnam. COMPOSE (2019-2021) and CounterMEASUREII (2021-2022) projects

[Lien vers la fiche source] Microplastic (300-5000µm) concentrations were measured in the Red River, the Nhue River (upstream, middle stream and downstream), the To Lich River and the Day River of Hanoi, Northern Vietnam, under the COMPOSE project (2019-2021) and the CounterMEASUREII project (2021-2022). Microplastic were sampled using a 80µm mesh size net from a local boat. The samples were extracted in the laboratory using enzymatic digestion, NaCl density separation and were filtrated on GF-A filter. Then microplastic were observed on stereomicroscope and length, area, color were measured for fragments, line and circle. Concentrations are given in total microplastic per m3, fragment per m3 and fibers per m3. The sampling dates are October 2019, January 2020, July 2020, October 2020, January 2021 and March 2021 under COMPOSE Project; November 2021 and January 2022 under the CounterMEASUREII project.
Cartographie des unités paysagères à partir de données satellitaires à Madagascar entre 2016 et 2020

[Lien vers la fiche source] La cartographie des paysages est cruciale pour le suivi et la compréhension d'un large éventail de processus, et pour relever des défis tels que l'aménagement du territoire, l'évaluation de la biodiversité, les interactions santé-environnement, et le suivi/évaluation des impacts des politiques de gestion de l'environnement et des ressources. Afin de développer une "reconnaissance de l'approche paysagère" opérationnelle, nous devons développer des cadres méthodologiques et des outils dédiés à la caractérisation et à la cartographie des paysages. Le [Centre d'Expertise Scientifique (CES) Paysage] du [Pôle Théia], auquel est rattaché ce projet TOSCA du même nom, a pour ambition de développer des produits et des services qui rendent robustes et transférables l'analyse des paysages dans une diversité de domaine nécessitant la prise en compte de l'activité humaine sur des milieux donnés et auprès des gestionnaires qui mobilisent déjà cet objet intégrateur en aménagement du territoire. #### Ce projet consiste à développer une méthode automatisée de délimitation des Unités Paysagères (UP) à partir de Variables Essentielles Paysagères (VEP) issues des données Copernicus. Ce premier volet du projet TOSCA vise à déterminer des méthodes pour délimiter les paysages. Une première méthode est donc proposée dans ce jeu de données. Vous pourrez retrouver les éléments suivants : - un schéma général récapitulatif de la méthode ; - l'ensemble des données mobilisées avec une série chronologique MODIS NDVI (produit MOD13Q1 pendant la période 2016-2020) et de données Sentinel-2 (2019) ; - la cartographie des unités paysagères finale réalisée avec la méthode sur la zone test choisie ; - un poster scientifique présenté au congrès INTECOL-2022 (cf. publication connexe).
Hydroclimatic vulnerability of peat carbon in the central Congo Basin: codes for age-depth models, geospatial data processing and analysis

[Lien vers la fiche source] This dataset includes two packages: 'Age_depth_models' and 'Tropical_Peats' for the creation of the age-depth models and the processing and analysis of the geospatial data, which are presented in the article "Hydroclimatic vulnerability of peat carbon in the central Congo Basin". The package 'Age_depth_models' includes the data and R codes to run the age/depth models of cores CEN-17.4, LOK5-5 and BDM1-7. The package 'Tropical_Peats' (JupyterHub notebooks [https://jupyter.org]) includes all the codes for the processing and analysis of the climate spaces (precipitation amount and seasonality index), tropical peatland distribution and precipitation reconstruction. In summary, the data processing starts with the upload of the CHELSA data Version 1.2 (climatologies) publicly available at [https://chelsa-climate.org/downloads/] and of the PEATMAP dataset (current geographical extents of peat-bearing regions) publicly available at [https://archive.researchdata.leeds.ac.uk/251/]. Then the data are reprojected (if necessary) and downsampled, the tropical areas are extracted, matched, analysed and ultimately plotted. Note that the sedimentary data presented in this study are available at [https://doi.pangaea.de/10.1594/PANGAEA.938019].
Analyses of soils sampled on Madagascar Highlands following temperature and rainfall gradients in 2014

[Lien vers la fiche source] Priming effect (PE) in soil is proposed to be generated by two distinct mechanisms: “stoichiometric decomposition” and/or “nutrient mining” theories. Each mechanism gets its own dynamics, involves its own microbial actors and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each PE generation mechanism via the modification of microbial and physicochemical soil properties. Soils were sampled (May 2014) in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic soil descriptors were Bulk Density, granulometry (clay silt and sand %), soil humidity, pH, CEC, oxydable Aluminium and Iron (estimation from spectral data) Kaolinite and Gibbsite content (estimations from spectral data), Total C, N and P, mineral N (addition of NH3 and NH4 data), available P. Biotic descriptors were microbial biomass phosphorus (MBP), molecular microbial biomass (MMB), 16S and 18S copy numbers per g of soil (qPCR), and bacterial and fungal communities composition (at the phylum level) obtained by 454 pyrosequencing methodology. DNA sequences were deposited in the European Nucleotide Archive, under the study accession number [PRJEB19651]. Soil respiration, wheat straw mineralization, and induced Priming effect have been recorded after a 7 and 42 days of soils laboratory incubation. All methodologies are described in the attached paper.
Geographical mapping of food outlets and foods and beverages advertised in Kenya

[Lien vers la fiche source] The aim of this study was to characterise the local foods and beverages sold and advertised in a deprived urban neighbourhood in Nairobi, Kenya. In 2017, a cross-sectional observational study design was used to audit all food outlets (outlet type and food type sold) and food advertisements. Data available on: types of foods and beverages sold and/or advertised in food outlets. A total of 499 food outlets or adverts were identified and assessed in Nairobi.
Native plants reported as threatened by identified alien plants in the global IUCN Red List

[Lien vers la fiche source] This dataset includes 1,407 pairs of threatened native–invasive alien plants extracted from the IUCN Red List of Threatened Species ([https://www.iucnredlist.org/]). For each pair, the threat category of the threatened native species (NT, VU, EN, CR, EW, EX), its population trend (increasing, stable, decreasing, unknown), whether the native species is restricted to islands (yes, no, partially) and whether the native species has been classified as threatened based exclusively on IUCN-red-list criterion B (restricted geographic range size) are specified. The R code of the analyses performed in the paper is provided in a second file.
Intense pressure on small and juvenile coral reef fishes threatens fishery production in Madagascar

[Lien vers la fiche source] The dataset includes a sample of fishery data on reef fish catches (catch per fishing trip, fish length, and catch composition at family level), minimal length at maturity for reef fishes, and fisher census in the Bay of Toliara, southwest Madagascar. These data were collected as part of a participatory survey from May 2018 to April 2019 at 8 villages in the Bay of Toliara. Specifically, 4 data files are provided: (1) suivi_part_toliara.xlsx ; (2) dt_station.csv ; (3) Juvenile_size_family2.csv; (4) pecheur_baie_toliara.xlsx Each data file is described in the attached documentation This dataset also include the R code that was used for processing this data.
Evaluation data for a multi-sectoral program to improve the resilience of households in Madagascar

[Lien vers la fiche source] Data were collected in southern Madagascar between 2018 and 2019 from a cohort of 600 households. They were collected as part of a project to evaluate a multi-sectoral program set up by the [World Food Program (WFP)] with the objective of improving the resilience of households in Madagascar. The Committee of Ethics of Biomedical Research of Madagascar approved the survey protocol. A Data Plan Management was prepared, as provided. Data were collected in tree times, respectively: - From 02/oct to 13/oct/2018 for the first pass - From 18/apr to 30/apr/2019 for the second pass - From 18/oct to 04/nov/2019 for the last pass. The information collected includes: * socio-demographic and economic data of households: household composition, education, religion, nature and amounts of income, means of production, information on housing, property owned, water supply and waste management; * module on household food security, resilience to shocks and coping strategies: FIES (Food Insecurity Experience Scale), shocks in the last 12 months, livelihoods, RCSI (Reduced Coping Strategy Index); * household Food Module: FCS (Food Consumption Score), HDDS (Household Dietary Diversity Score); * household education (systematically assessed for children aged 6 to 15 in the household): school attendance, grade level, absenteeism, school lunch; * household exposure to different interventions: PREVMAM/Nut-Stunting, Food For Assets and school canteens; * at the level of mother-child couples: reproductive history, knowledge, decision-making power and dietary diversity of the woman, feeding practices of the young child (Infant and Young Child Feeding Indicators), detection and management of child malnutrition. This dataset includes 4 databases according to the level of collection: - PROCOR_Database_AgriculturalLand_Madagascar_2018_2019.tab - PROCOR_Database_MembersOfHousehold_Madagascar_2018_2019.tab - PROCOR_Database_MotherChild_Madagascar_2018_2019.tab - PROCOR_Database_Household_Madagascar_2018_2019.tab